LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-217-g1909233c69-modified)
  using 1 OpenMP thread(s) per MPI task
# The intention is to find the average position of one wall at atmospheric
# pressure.  The output is the wall position over time which can be used to
# find the average position for a run with fixed wall position.
#
# ----------------- Init Section -----------------

atom_style    full
units         real
boundary      p p f
kspace_style  pppm/electrode 1e-4
kspace_modify slab 3.0
pair_style    lj/cut/coul/long 8 8
bond_style    harmonic
angle_style   harmonic
if "$(extract_setting(world_size) % 2) == 0" then "processors * * 2"

# ----------------- Atom Definition Section -----------------

read_data "data.piston"
Reading data file ...
  orthogonal box = (0 0 0) to (17.6494 20.3798 26)
  1 by 1 by 1 MPI processor grid
  reading atoms ...
  726 atoms
  reading velocities ...
  726 velocities
  scanning bonds ...
  2 = max bonds/atom
  scanning angles ...
  1 = max angles/atom
  reading bonds ...
  420 bonds
  reading angles ...
  210 angles
Finding 1-2 1-3 1-4 neighbors ...
  special bond factors lj:    0        0        0       
  special bond factors coul:  0        0        0       
     2 = max # of 1-2 neighbors
     1 = max # of 1-3 neighbors
     1 = max # of 1-4 neighbors
     2 = max # of special neighbors
  special bonds CPU = 0.000 seconds
  read_data CPU = 0.012 seconds

# ----------------- Settings Section -----------------

pair_coeff 1 1 0.069 2.78
pair_coeff 2 2 5.29 2.951
pair_coeff 3 3 0.1553 3.166
pair_coeff 4 4 0.0 0.0
bond_coeff 1 600.0 1.0
angle_coeff 1 75.0 109.47
group wall type 1
48 atoms in group wall
group gold type 2
48 atoms in group gold
group spce type 3:4
630 atoms in group spce
group ele union wall gold
96 atoms in group ele
fix fRattleSPCE spce shake 0.0001 10 0 b 1 a 1
Finding SHAKE clusters ...
       0 = # of size 2 clusters
       0 = # of size 3 clusters
       0 = # of size 4 clusters
     210 = # of frozen angles
  find clusters CPU = 0.000 seconds
pair_modify mix arithmetic

# ----------------- Run Section -----------------

neigh_modify every 1 delay 0
timestep 2
fix fxnvt      spce nvt temp 300 300 500
fix fxforce_au gold setforce 0.0 0.0 0.0

# equilibrate z-coordinate of upper electrode while keeping the electrode rigid
fix fxforce_wa wall setforce 0.0 0.0 NULL
variable atm equal 1/68568.415 # 1/force->nktv2p
variable area equal (xhi-xlo)*(yhi-ylo)
variable wall_force equal -v_atm*v_area/count(wall)
print "Wall force per atom: ${wall_force}"
Wall force per atom: -0.000109285996244287
fix fxpressure wall aveforce 0 0 ${wall_force} # atomspheric pressure: area/force->nktv2p
fix fxpressure wall aveforce 0 0 -0.000109285996244287 
fix fxdrag     wall viscous 100
fix fxrigid    wall rigid/nve single
  1 rigid bodies with 48 atoms

# maintain constant potential during equilibration
# 'algo cg' allows for moving electrodes
fix fxele      ele electrode/conp 0.0 1.805 symm on algo cg 1e-4
96 atoms in group conp_group

# setup output and run
variable q atom q
compute qwa wall reduce sum v_q
compute qau gold reduce sum v_q
variable top_wall equal (bound(wall,zmin))
compute temp_mobile spce temp
variable s equal step
fix fxprint    all print 1000 "${s} ${top_wall}" file top_wall.csv screen no
thermo_style custom step c_temp_mobile c_qwa c_qau v_top_wall
thermo 5000
run 100000

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

Your simulation uses code contributions which should be cited:

- kspace_style pppm/electrode command:

@article{Ahrens2021,
author = {Ahrens-Iwers, Ludwig J.V. and Mei{\ss}ner, Robert H.},
doi = {10.1063/5.0063381},
title = {{Constant potential simulations on a mesh}},
journal = {Journal of Chemical Physics},
year = {2021}
volume = {155},
pages = {104104},
}
- fix electrode command:

@article{Ahrens2022
author = {Ahrens-Iwers, Ludwig J.V. and Janssen, Mahijs and Tee, Shern R. and Mei{\ss}ner, Robert H.},
doi = {10.1063/5.0099239},
title = {{ELECTRODE: An electrochemistry package for LAMMPS}},
journal = {The Journal of Chemical Physics},
year = {2022}
volume = {157},
pages = {084801},
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

PPPM/electrode initialization ...
  using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
  G vector (1/distance) = 0.32814871
  grid = 12 15 36
  stencil order = 5
  estimated absolute RMS force accuracy = 0.02930901
  estimated relative force accuracy = 8.8263214e-05
  using double precision FFTW3
  3d grid and FFT values/proc = 15884 6480
Generated 6 of 6 mixed pair_coeff terms from arithmetic mixing rule
Neighbor list info ...
  update: every = 1 steps, delay = 0 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 10
  ghost atom cutoff = 10
  binsize = 5, bins = 4 5 6
  2 neighbor lists, perpetual/occasional/extra = 2 0 0
  (1) pair lj/cut/coul/long, perpetual
      attributes: half, newton on
      pair build: half/bin/newton
      stencil: half/bin/3d
      bin: standard
  (2) fix electrode/conp, perpetual, copy from (1)
      attributes: half, newton on
      pair build: copy
      stencil: none
      bin: none
Per MPI rank memory allocation (min/avg/max) = 11.7 | 11.7 | 11.7 Mbytes
   Step     c_temp_mobile      c_qwa          c_qau        v_top_wall  
         0   303.38967     -0.042963484    0.042963484    21.4018      
      5000   311.85363      0.03543775    -0.03543775     24.79665     
     10000   285.91321     -0.16873703     0.16873703     23.103088    
     15000   295.39476     -0.44424612     0.44424612     23.767107    
     20000   296.12969     -0.14120993     0.14120993     23.96361     
     25000   306.59629     -0.29333182     0.29333182     23.884488    
     30000   297.98559     -0.10749684     0.10749684     23.73316     
     35000   297.98503     -0.11809975     0.11809975     23.984669    
     40000   300.26292     -0.32784184     0.32784184     23.462748    
     45000   295.68441     -0.25940165     0.25940165     23.516403    
     50000   315.12883     -0.36037614     0.36037614     23.627879    
     55000   290.55151     -0.0032838106   0.0032838106   23.684931    
     60000   316.4625      -0.17245368     0.17245368     24.126883    
     65000   296.79343     -0.054061851    0.054061851    23.695094    
     70000   305.99923     -0.11363801     0.11363801     23.55476     
     75000   297.40131     -0.27054153     0.27054153     23.928994    
     80000   306.54811     -0.25409719     0.25409719     23.869448    
     85000   303.95231     -0.17895561     0.17895561     23.658833    
     90000   313.43739     -0.059036514    0.059036514    23.36056     
     95000   290.3077      -0.31394478     0.31394478     23.885538    
    100000   297.5156      -0.30730083     0.30730083     23.511674    
Loop time of 1586.06 on 1 procs for 100000 steps with 726 atoms

Performance: 10.895 ns/day, 2.203 hours/ns, 63.049 timesteps/s, 45.774 katom-step/s
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 460.91     | 460.91     | 460.91     |   0.0 | 29.06
Bond    | 0.047873   | 0.047873   | 0.047873   |   0.0 |  0.00
Kspace  | 341.4      | 341.4      | 341.4      |   0.0 | 21.53
Neigh   | 52.868     | 52.868     | 52.868     |   0.0 |  3.33
Comm    | 5.2321     | 5.2321     | 5.2321     |   0.0 |  0.33
Output  | 0.00099102 | 0.00099102 | 0.00099102 |   0.0 |  0.00
Modify  | 724.63     | 724.63     | 724.63     |   0.0 | 45.69
Other   |            | 0.9741     |            |       |  0.06

Nlocal:            726 ave         726 max         726 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:           2336 ave        2336 max        2336 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:         120321 ave      120321 max      120321 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 120321
Ave neighs/atom = 165.7314
Ave special neighs/atom = 1.7355372
Neighbor list builds = 7670
Dangerous builds = 0
write_data "data.piston.final"
System init for write_data ...
PPPM/electrode initialization ...
  using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
  G vector (1/distance) = 0.32814871
  grid = 12 15 36
  stencil order = 5
  estimated absolute RMS force accuracy = 0.029311329
  estimated relative force accuracy = 8.8270197e-05
  using double precision FFTW3
  3d grid and FFT values/proc = 15884 6480
Generated 6 of 6 mixed pair_coeff terms from arithmetic mixing rule

Average conjugate gradient steps: 1.981
Total wall time: 0:26:26
